The digital PCR instrument is a digital instrument for amplifying and amplifying specific DNA fragments. The problem studied in this paper is the autofocus problem of its electronic imaging device. Based on the analysis of existing SOM neural network autofocus scheme, we propose an improved scheme-BP neural network for autofocus. It directly takes the SOM input and the actual focus position as the input and output of the BP neural network, which eliminates the process of prior classification and then corresponding to the focus matrix in the original SOM scheme, saving time. The experimental results show that the traditional autofocus method has good focusing effect, but the speed is slow, and the universality of the BP neural network autofocus scheme is not good enough, but within a good accuracy range, the speed is faster. Compared to traditional focusing methods, the autofocus scheme designed in this paper successfully achieves faster focusing speed for biochips.